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authorThomas White <taw@physics.org>2010-11-18 15:27:13 +0100
committerThomas White <taw@physics.org>2012-02-22 15:27:06 +0100
commitcf074c7d62721ce324dfac93c1c9fca45577c142 (patch)
treed619c78ec71cbfc3d139ea63bc54cef32800a190
parent66824469cd43ce5dcc7df58f631ce1791dc7058c (diff)
facetron: Initial refinement stuff
-rw-r--r--src/facetron.c201
-rw-r--r--src/image.h2
2 files changed, 200 insertions, 3 deletions
diff --git a/src/facetron.c b/src/facetron.c
index f4148ae1..ca58ea2a 100644
--- a/src/facetron.c
+++ b/src/facetron.c
@@ -22,6 +22,9 @@
#include <getopt.h>
#include <assert.h>
#include <pthread.h>
+#include <gsl/gsl_matrix.h>
+#include <gsl/gsl_vector.h>
+#include <gsl/gsl_linalg.h>
#include "utils.h"
#include "hdf5-file.h"
@@ -34,6 +37,13 @@
#include "beam-parameters.h"
+/* Refineable parameters */
+enum {
+ REF_SCALE,
+ NUM_PARAMS
+};
+
+
static void show_help(const char *s)
{
printf("Syntax: %s [options]\n\n", s);
@@ -68,11 +78,197 @@ struct refine_args
};
+/* Return the gradient of parameter 'k' given the current status of 'image'. */
+static double gradient(struct image *image, int k,
+ struct cpeak spot, double I_partial)
+{
+ switch ( k ) {
+
+ case REF_SCALE :
+ return I_partial;
+
+ }
+
+ ERROR("No gradient defined for parameter %i\n", k);
+ abort();
+}
+
+
+/* Apply the given shift to the 'k'th parameter of 'image'. */
+static void apply_shift(struct image *image, int k, double shift)
+{
+ switch ( k ) {
+
+ case REF_SCALE :
+ image->osf += shift;
+ break;
+
+ default :
+ ERROR("No gradient defined for parameter %i\n", k);
+ abort();
+
+ }
+}
+
+
+static double mean_partial_dev(struct image *image, struct cpeak *spots, int n,
+ const char *sym, double *i_full)
+{
+ int h;
+ double delta_I;
+
+ for ( h=0; h<n; h++ ) {
+
+ signed int hind, kind, lind;
+ signed int ha, ka, la;
+ double I_full;
+ float I_partial;
+ float xc, yc;
+
+ hind = spots[h].h;
+ kind = spots[h].k;
+ lind = spots[h].l;
+
+ /* Don't attempt to use spots with very small
+ * partialities, since it won't be accurate. */
+ if ( spots[h].p < 0.1 ) continue;
+
+ /* Actual measurement of this reflection from this
+ * pattern? */
+ /* FIXME: Coordinates aren't whole numbers */
+ if ( integrate_peak(image, spots[h].x, spots[h].y,
+ &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
+ continue;
+ }
+
+ get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
+ I_full = lookup_intensity(i_full, ha, ka, la);
+ delta_I += I_partial - spots[h].p * I_full;
+
+ }
+
+ return delta_I / (double)n;
+}
+
+
+static double iterate(struct image *image, double *i_full, const char *sym,
+ struct cpeak *spots, int n)
+{
+ gsl_matrix *M;
+ gsl_vector *v;
+ gsl_vector *shifts;
+ int h, shift;
+
+ M = gsl_matrix_alloc(NUM_PARAMS, NUM_PARAMS);
+ v = gsl_vector_alloc(NUM_PARAMS);
+
+ /* Construct the equations, one per reflection in this image */
+ for ( h=0; h<n; h++ ) {
+
+ signed int hind, kind, lind;
+ signed int ha, ka, la;
+ double I_full, delta_I;
+ float I_partial;
+ float xc, yc;
+ int k;
+
+ hind = spots[h].h;
+ kind = spots[h].k;
+ lind = spots[h].l;
+
+ /* Don't attempt to use spots with very small
+ * partialities, since it won't be accurate. */
+ if ( spots[h].p < 0.1 ) continue;
+
+ /* Actual measurement of this reflection from this
+ * pattern? */
+ /* FIXME: Coordinates aren't whole numbers */
+ if ( integrate_peak(image, spots[h].x, spots[h].y,
+ &xc, &yc, &I_partial, NULL, NULL, 1, 1) ) {
+ continue;
+ }
+
+ get_asymm(hind, kind, lind, &ha, &ka, &la, sym);
+ I_full = lookup_intensity(i_full, ha, ka, la);
+ delta_I = I_partial - spots[h].p * I_full;
+
+ for ( k=0; k<NUM_PARAMS; k++ ) {
+
+ int g;
+ double v_c;
+
+ for ( g=0; g<NUM_PARAMS; g++ ) {
+
+ double M_curr, M_c;
+
+ M_curr = gsl_matrix_get(M, g, k);
+
+ M_c = gradient(image, g, spots[h], I_partial)
+ * gradient(image, k, spots[h], I_partial);
+ M_c *= pow(I_full, 2.0);
+
+ gsl_matrix_set(M, g, k, M_curr + M_c);
+
+ }
+
+ v_c = delta_I * I_full * gradient(image, k, spots[h],
+ I_partial);
+ gsl_vector_set(v, k, v_c);
+
+ }
+
+ }
+
+ shifts = gsl_vector_alloc(NUM_PARAMS);
+ gsl_linalg_HH_solve(M, v, shifts);
+ for ( shift=0; shift<NUM_PARAMS; shift++ ) {
+ apply_shift(image, shift, gsl_vector_get(shifts, shift));
+ }
+
+ free(spots);
+ spots = find_intersections(image, image->indexed_cell, &n, 0);
+ return mean_partial_dev(image, spots, n, sym, i_full);
+}
+
+
static void refine_image(int mytask, void *tasks)
{
struct refine_args *all_args = tasks;
struct refine_args *pargs = &all_args[mytask];
- /* Do, er, something. */
+ struct image *image = pargs->image;
+ double nominal_photon_energy = pargs->image->beam->photon_energy;
+ struct hdfile *hdfile;
+ struct cpeak *spots;
+ int n;
+ double dev;
+
+ hdfile = hdfile_open(image->filename);
+ if ( hdfile == NULL ) {
+ ERROR("Couldn't open '%s'\n", image->filename);
+ return;
+ } else if ( hdfile_set_image(hdfile, "/data/data0") ) {
+ ERROR("Couldn't select path\n");
+ hdfile_close(hdfile);
+ return;
+ }
+
+ if ( hdf5_read(hdfile, pargs->image, 0, nominal_photon_energy) ) {
+ ERROR("Couldn't read '%s'\n", image->filename);
+ hdfile_close(hdfile);
+ return;
+ }
+
+ spots = find_intersections(image, image->indexed_cell, &n, 0);
+ dev = iterate(image, pargs->i_full, pargs->sym, spots, n);
+ STATUS("Iteration %2i: mean dev = %5.2f\n", 0, dev);
+
+ free(image->data);
+ if ( image->flags != NULL ) free(image->flags);
+ hdfile_close(hdfile);
+
+ /* Muppet proofing */
+ image->data = NULL;
+ image->flags = NULL;
}
@@ -114,7 +310,7 @@ static void integrate_image(int mytask, void *tasks)
}
/* Figure out which spots should appear in this pattern */
- spots = find_intersections(image, image->indexed_cell, &n, 0);
+ spots = find_intersections(image, image->indexed_cell, &n, 1);
/* For each reflection, estimate the partiality */
for ( j=0; j<n; j++ ) {
@@ -414,6 +610,7 @@ int main(int argc, char *argv[])
images[i].bw = beam->bandwidth;
images[i].det = det;
images[i].beam = beam;
+ images[i].osf = 1.0;
/* Muppet proofing */
images[i].data = NULL;
diff --git a/src/image.h b/src/image.h
index 6b09dfc4..ae2f3179 100644
--- a/src/image.h
+++ b/src/image.h
@@ -94,7 +94,6 @@ struct image {
/* Information about the crystal */
double m; /* Mosaicity in radians */
-
/* Per-shot radiation values */
double lambda; /* Wavelength in m */
double div; /* Divergence in radians */
@@ -102,6 +101,7 @@ struct image {
double f0; /* Incident intensity */
int f0_available; /* 0 if f0 wasn't available
* from the input. */
+ double osf; /* Overall scaling factor */
int width;
int height;